I've been having some issues getting R to run properly on the shared cluster at my institution , where i don't have root access. Some things will work but it gets tricky when i need to install packages etc. The current issue i'm trying to trouble shoot is the following error when trying to load the caret package:
Loading required package: lattice
Loading required package: ggplot2
Error: package or namespace load failed for ‘ggplot2’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/cifs/hariri-long/Scripts/Tools/R/packages/rlang/libs/rlang.so':
/cifs/hariri-long/Scripts/Tools/R/packages/rlang/libs/rlang.so: undefined symbol: R_removeVarFromFrame
Error: package ‘ggplot2’ could not be loaded
Execution halted
I found this page suggesting i install rlang as follows:
> install.packages("rlang",type="source")
Installing package into ‘/cifs/hariri-long/Scripts/Tools/R/packages’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Error: .onLoad failed in loadNamespace() for 'tcltk', details:
call: fun(libname, pkgname)
error: Can't find a usable init.tcl in the following directories:
/usr/share/tcl8.5 ./lib/tcl8.5 ./lib/tcl8.5 ./library ./library ./tcl8.5.13/library ./tcl8.5.13/library
but i get the above tcl error. since i've seen this in other threads:
> capabilities("tcltk")
tcltk
TRUE
it looks like tcl on my system is 8.6, but i don't know how to tell R to look for that version.
$ whereis tcl
tcl: /usr/lib64/tcl8.6 /usr/include/tcl.h /usr/share/tcl8.6
$ which R
/opt/apps/rhel7/R-3.6.0/bin/R
Any ideas? The OS is CentOS 8. Thanks!
I ended up deciding to try using a more recent R version (4.1.1) to solve this issue. I was hesitant to do this at first because I have run into issues with availability / compatibility of packages I need in more recent R versions, but I wasn't getting anywhere troubleshooting this issue otherwise. I figured that since TCL 8.6 is what was installed on the system, a newer version of R might be able to work with it, and seems i was right, since I got past the first error I was having when I switched.
I did get a new error regarding an issue loading the shared library Libtk8.6.so. So I downloaded the .so file from here and unpacked it to my home directory using rpm2cpio (i don't have root access so i can't just use yum install etc). After that i just had to re-install all my packages for the new R version and it worked!
Related
I have been trying to install the rgl package in my macOS Big Sur, but I have failed each time.
I have downloaded R from the CRAN website, and have also installed Xquartz. After rebooting the computer, I tried to install the rgl package from the R console. It installs successfully, but whenever I type library("rgl") in the R console, the package does not load, and instead, this is shown :
Error in dyn.load(dynlib <- getDynlib(dir)) :
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/rgl/libs/rgl.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/rgl/libs/rgl.so, 6): Symbol not found: _hb_buffer_add_utf8
Referenced from: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/rgl/libs/rgl.so
Expected in: flat namespace
in /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/rgl/libs/rgl.so
Error: package or namespace load failed for ‘rgl’:
.onLoad failed in loadNamespace() for 'rgl', details:
call: rgl.init(initValue, onlyNULL)
error: OpenGL is not available in this build
In addition: Warning messages:
1: Loading rgl's DLL failed.
This build of rgl depends on XQuartz, which failed to load.
See the discussion in https://stackoverflow.com/a/66127391/2554330
2: Trying without OpenGL...
I headed to the link that this error message mentions, and tried uninstalling rgl and Xquartz, and reinstalling them again, but the issue remains.
Moreover, here it is said that I am supposed to delete org.xquartz.startx.plist from /Library/LaunchDaemons, but from the terminal, after navigating to the Library directory, it seems that there is nothing named LaunchDaemons or LaunchAgents.
Any help would be appreciated. I am using macOS Big Sur 11.4, Xquartz 2.8.1 and rgl 0.106.8. Thanks.
System: Ubuntu 18.04
Original error that showed up that prompted me to try to reinstall R and dependencies:
Error: package or namespace load failed for 'lubridate' in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/usr/local/lib/R/site-library/stringi/libs/stringi.so': libicui18n.so.57: cannot open shared object file: No such file or directory
Steps to reproduce:
Install R: apt install r-base
Try to install R dependencies: install.packages(c("dplyr", "lubridate", "qcc", "forecast"), repos='http://cran.us.r-project.org')
Error that displays during installation:
/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated
Error that displays after installation:
The downloaded source packages are in
'/tmp/RtmpnulsEe/downloaded_packages'
Warning message:
In install.packages(c("dplyr", "lubridate", "qcc", "forecast", "stringi"), :
installation of package 'forecast' had non-zero exit status
After purging and reinstalling r-base and R dependencies, I'm seeing this...(already checked that libcurl4-openssl-dev was latest version):
Error: package or namespace load failed for 'forecast' in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/local/lib/R/site-library/curl/libs/curl.so':
/usr/lib/x86_64-linux-gnu/libcurl.so.4: version `CURL_OPENSSL_3' not found (required by /usr/local/lib/R/site-library/curl/libs/curl.so)
Update: Apparently it's something in the forecast library, because I reproduced that error like this:
$ R
> library(forecast)
Error: package or namespace load failed for 'forecast' in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/local/lib/R/site-library/curl/libs/curl.so':
/usr/lib/x86_64-linux-gnu/libcurl.so.4: version `CURL_OPENSSL_3' not found (required by /usr/local/lib/R/site-library/curl/libs/curl.so)
Your original problem is that stringi was built against a distro package version of libicu which changed. As this distribution package does not know you have lubridate in /usr/local it changes and breaks things.
There are a number of ways to fix this. The easiest (and narrowest) is to make sure you have libicu-dev installed. You could then reinstall (ie: rebuild stringi) after which lubridate will load.
For the rest you are just going somewhat wild throwing everything that is moveable up against the wall. You need to take a moment to realize that you can either install all these as binaries (ie from the Michael Rutter PPAs at launchpad), or from source. Your call. I have an older answer explaining the difference here (as well as in other follow-ups here) and we help on the r-sig-debian list too.
But in short: read this README at CRAN (esp first few paragraphs) and consider the PPAs.
After trying the following (purging and reinstalling R between each step):
apt purge r-base
Added/removed several different PPAs before realizing none of them supported Bionic Beaver. Result: Release not found.
Found Michael Rutter's PPA and attempted to use that. Result: same error message from above ('CURL_OPENSSL_3' not found).
Attempting several solutions to this SO article. Result: same error message from above ('CURL_OPENSSL_3' not found).
Read this article and performed the following in R:
> remove.packages("curl")
> install.packages("curl")
> install.packages(c("dplyr", "lubridate", "qcc", "forecast", "stringi", "curl"), repos='http://cran.us.r-project.org')
And everything worked as intended.
I'm running on Ubuntu 16.04 (on a Lenovo ThinkPak T450). I have installed R version 3.4.1, installed by following the instructions here via Rbloggers.
From here, I would like to start installing packages, but if I run R from the command line without root privileges, I cannot access a CRAN mirror. That is, when I run install.packages('dplyr') (or any install.packages('blah')) I get the following error
--- Please select a CRAN mirror for use in this session ---
Error: .onLoad failed in loadNamespace() for 'tcltk', details:
call: fun(libname, pkgname)
error: Can't find a usable init.tcl in the following directories:
/opt/anaconda1anaconda2anaconda3/lib/tcl8.5 ./lib/tcl8.5 ./lib/tcl8.5 ./library ./library ./tcl8.5.18/library ./tcl8.5.18/library
With that error, no CRAN mirror dialog box appears and hence no installation of packages. Note: this error does not happen when I start R with root privileges (i.e., start via > sudo R), but I do not want to install packages as root.
Thanks in advance for any help you can send my way!
Edit: Specifying the repo also results in error (in the file paths below, I replaced my user-name with user-name).
E.g.: install.packages('Rcpp',repos='http://cran.us.r-project.org') terminates with:
installing to /home/user-name/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error: package or namespace load failed for ‘Rcpp’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/user-name/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/libs/Rcpp.so':
/home/user-name/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/libs/Rcpp.so: undefined symbol: _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEED1Ev
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/user-name/R/x86_64-pc-linux-gnu-library/3.4/Rcpp’
E.g., install.packages('dplyr',repos='http://cran.us.r-project.org') terminates with:
installing to /home/user-name/R/x86_64-pc-linux-gnu-library/3.4/dplyr/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/user-name/R/x86_64-pc-linux-gnu-library/3.4/bindrcpp/libs/bindrcpp.so':
/home/user-name/anaconda3/lib/R/bin/exec/../../lib/../.././libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /home/user-name/R/x86_64-pc-linux-gnu-library/3.4/bindrcpp/libs/bindrcpp.so)
ERROR: lazy loading failed for package ‘dplyr’
* removing ‘/home/user-name/R/x86_64-pc-linux-gnu-library/3.4/dplyr’
As pointed out by DirkEddelbuettel in the comments, the issue was a mixing of Anaconda and R. To fix this problem:
I uninstalled the R packages from Anaconda by first looking at > conda list and realizing that the package was r-base; hence running > conda remove r-base.
Next, by looking at the output of > which R, it was clear that we were still trying to execute from the ../anaconda3/bin/.. directory. I suspect there is a quick way to change this via an export or bashrc amendment (or something similar), but for me, the quickest work-around was to run > sudo apt-get install r-base r-base-dev, which took all of 0.2 seconds as they were already installed, but it did affect the directory which the system looks in to the appropriate one, for me this is /usr/bin/R/.
From here I've been able to install everything I've needed.
Note: Thinking back, I suspect the "mixing" happened when I installed rpy2 via conda.
Bear in mind that I am computer illiterate and new to R. I have installed the rJava package in R studio version 1.0.143 and installed Java 8 (using MacOS Sierra). When I try to load the rJava package:
library(rJava)
I get the following error
Unable to find any JVMs matching version "(null)".
No Java runtime present, try --request to install.
Error: package or namespace load failed for ‘rJava’:
.onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object
'/Users/cormac/Library/R/3.4/library/rJava/libs/rJava.so':
dlopen(/Users/cormac/Library/R/3.4/library/rJava/libs/rJava.so, 6):
Library not loaded: #rpath/libjvm.dylib
Referenced from:
/Users/cormac/Library/R/3.4/library/rJava/libs/rJava.so
Reason: image not found
In addition: Warning messages:
1: package ‘rJava’ was built under R version 3.4.2
2: running command '/usr/libexec/java_home' had status 1
Could somebody help me to interpret this error message? There is probably a very simple solution, but I am completely lost. Thank you!!
As noted in Unable to load rJava in RStudio, there is a very specific sequence of steps that must be taken to get rJava to work on a Macbook, as documented in rJava Issues #86.
Download and install Java from Oracle
Uninstall any previously installed version of rJava
Add JAVA_HOME to your .bashrc
Close & restart terminal, R and RStudio sessions so they pick up the updated JAVA_HOME
Use install.packages() to install rJava
See the URL link above for additional details on each step.
I was able to download the package "LMERConvenienceFunctions"
The downloaded binary packages are in
/var/folders/2p/3h5yk1gx4fs1gd8gtdbhdd900000gn/T//RtmpHvJyRm/downloaded_packages
However when I try to call it using:
library(LMERConvenienceFunctions)
I get the following error:
Error : .onLoad failed in loadNamespace() for 'rgl', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object'/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rgl/libs/rgl.so': dlopen(/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rgl/libs/rgl.so, 6):
Library not loaded: /opt/X11/lib/libGLU.1.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rgl/libs/rgl.so
Reason: image not found
Error: package or namespace load failed for ‘LMERConvenienceFunctions’
Does anyone have any suggestions?
Thanks!
It seems like you have tried to install the "LMERConvenienceFunctions" package without also downloading it's dependencies? Running
install.packages("LMERConvenienceFunctions")
and then just using library(LMERConvenienceFunctions) worked for me in this case. If this still doesn't work, try manually installing rgl
My issue turned out to be that I didn't have XQuartz installed. It can be downloaded here: http://www.xquartz.org/
After installing it, rgl began to work, and then LMERConvenienceFunctions finally started working as well. The whole process took a few tweaks so I'm pasting the entire code below. Note that this is after installing XQuartz.
install.packages("LMERConvenienceFunctions")
install.packages("devtools") #not sure if this is necessary, but doing this before rgl was recommended on another answer on here#
library(devtools)
install.packages("rgl")
rgl.useNULL=TRUE #little thing I had to do even after installing XQuartz#
library(rgl)
library(LMERConvenienceFunctions)